[2023-06-08 12:36:44,520] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:36:44,522] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:36:44,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg44f14401-c339-4e72-9371-fdb0c60c578c/dqc_reference
[2023-06-08 12:36:45,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:36:45,747] [INFO] Task started: Prodigal
[2023-06-08 12:36:45,748] [INFO] Running command: gunzip -c /var/lib/cwl/stg269e6f18-a059-4026-a100-85d590affe00/GCA_902528875.1_AG-337-P19_genomic.fna.gz | prodigal -d GCA_902528875.1_AG-337-P19_genomic.fna/cds.fna -a GCA_902528875.1_AG-337-P19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:36:47,511] [INFO] Task succeeded: Prodigal
[2023-06-08 12:36:47,511] [INFO] Task started: HMMsearch
[2023-06-08 12:36:47,511] [INFO] Running command: hmmsearch --tblout GCA_902528875.1_AG-337-P19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44f14401-c339-4e72-9371-fdb0c60c578c/dqc_reference/reference_markers.hmm GCA_902528875.1_AG-337-P19_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:36:47,699] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:36:47,701] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg269e6f18-a059-4026-a100-85d590affe00/GCA_902528875.1_AG-337-P19_genomic.fna.gz]
[2023-06-08 12:36:47,718] [INFO] Query marker FASTA was written to GCA_902528875.1_AG-337-P19_genomic.fna/markers.fasta
[2023-06-08 12:36:47,718] [INFO] Task started: Blastn
[2023-06-08 12:36:47,719] [INFO] Running command: blastn -query GCA_902528875.1_AG-337-P19_genomic.fna/markers.fasta -db /var/lib/cwl/stg44f14401-c339-4e72-9371-fdb0c60c578c/dqc_reference/reference_markers.fasta -out GCA_902528875.1_AG-337-P19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:36:48,256] [INFO] Task succeeded: Blastn
[2023-06-08 12:36:48,260] [INFO] Selected 13 target genomes.
[2023-06-08 12:36:48,261] [INFO] Target genome list was writen to GCA_902528875.1_AG-337-P19_genomic.fna/target_genomes.txt
[2023-06-08 12:36:48,265] [INFO] Task started: fastANI
[2023-06-08 12:36:48,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg269e6f18-a059-4026-a100-85d590affe00/GCA_902528875.1_AG-337-P19_genomic.fna.gz --refList GCA_902528875.1_AG-337-P19_genomic.fna/target_genomes.txt --output GCA_902528875.1_AG-337-P19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:36:53,032] [INFO] Task succeeded: fastANI
[2023-06-08 12:36:53,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44f14401-c339-4e72-9371-fdb0c60c578c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:36:53,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44f14401-c339-4e72-9371-fdb0c60c578c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:36:53,036] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:36:53,036] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:36:53,037] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-08 12:36:53,040] [INFO] DFAST Taxonomy check result was written to GCA_902528875.1_AG-337-P19_genomic.fna/tc_result.tsv
[2023-06-08 12:36:53,040] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:36:53,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:36:53,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44f14401-c339-4e72-9371-fdb0c60c578c/dqc_reference/checkm_data
[2023-06-08 12:36:53,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:36:53,063] [INFO] Task started: CheckM
[2023-06-08 12:36:53,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902528875.1_AG-337-P19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902528875.1_AG-337-P19_genomic.fna/checkm_input GCA_902528875.1_AG-337-P19_genomic.fna/checkm_result
[2023-06-08 12:37:06,882] [INFO] Task succeeded: CheckM
[2023-06-08 12:37:06,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:37:06,904] [INFO] ===== Completeness check finished =====
[2023-06-08 12:37:06,904] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:37:06,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902528875.1_AG-337-P19_genomic.fna/markers.fasta)
[2023-06-08 12:37:06,905] [INFO] Task started: Blastn
[2023-06-08 12:37:06,905] [INFO] Running command: blastn -query GCA_902528875.1_AG-337-P19_genomic.fna/markers.fasta -db /var/lib/cwl/stg44f14401-c339-4e72-9371-fdb0c60c578c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902528875.1_AG-337-P19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:37:07,627] [INFO] Task succeeded: Blastn
[2023-06-08 12:37:07,637] [INFO] Selected 12 target genomes.
[2023-06-08 12:37:07,637] [INFO] Target genome list was writen to GCA_902528875.1_AG-337-P19_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:37:07,641] [INFO] Task started: fastANI
[2023-06-08 12:37:07,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg269e6f18-a059-4026-a100-85d590affe00/GCA_902528875.1_AG-337-P19_genomic.fna.gz --refList GCA_902528875.1_AG-337-P19_genomic.fna/target_genomes_gtdb.txt --output GCA_902528875.1_AG-337-P19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:37:10,273] [INFO] Task succeeded: fastANI
[2023-06-08 12:37:10,290] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:37:10,290] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902528875.1	s__SAR86A sp902528875	100.0	314	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902516285.1	s__SAR86A sp902516285	94.8542	255	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_002721465.1	s__SAR86A sp002721465	92.8629	226	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.78	96.78	0.69	0.69	2	-
GCA_902582355.1	s__SAR86A sp902582355	79.5408	84	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.87	98.87	0.67	0.67	2	-
GCA_004212975.1	s__SAR86A sp004212975	78.8529	90	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.30	95.02	0.85	0.76	8	-
GCA_902591925.1	s__SAR86A sp902591925	78.6257	120	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902520495.1	s__SAR86A sp902520495	78.4282	109	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690725.1	s__SAR86A sp002690725	77.6321	100	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	-
GCA_002710265.1	s__SAR86A sp002710265	77.6144	90	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213495.1	s__SAR86A sp003213495	77.3748	110	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902515155.1	s__SCGC-AAA076-P13 sp902515155	77.2948	72	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:37:10,292] [INFO] GTDB search result was written to GCA_902528875.1_AG-337-P19_genomic.fna/result_gtdb.tsv
[2023-06-08 12:37:10,292] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:37:10,295] [INFO] DFAST_QC result json was written to GCA_902528875.1_AG-337-P19_genomic.fna/dqc_result.json
[2023-06-08 12:37:10,295] [INFO] DFAST_QC completed!
[2023-06-08 12:37:10,295] [INFO] Total running time: 0h0m26s